fix cocoindex package dependency

README.md

@@ -42,6 +42,7 @@ pip install java-codebase-rag
 ```
 
 Python **3.11+** required. After install, `java-codebase-rag --help` should print the CLI groups.
+The package includes the CocoIndex lifecycle dependency used by `init`, `increment`, `reprocess`, and `erase`.
 
 > **Stability disclaimer.** This package does **not** promise backward compatibility. MCP tool contracts, env vars, Lance/Kuzu schemas, config files, and Python APIs may change without a deprecation period. Track `main` and rebuild indexes when ontology or embedding settings change.
 
@@ -199,7 +200,7 @@ python3 -m venv .venv
 .venv/bin/pip install -r requirements.txt
 ```
 
-The `cocoindex` package is **only** needed for lifecycle commands that run the indexer (`init`, `increment`, `reprocess`, `erase`). Search and MCP navigation work without it.
+The `cocoindex` package powers lifecycle commands that run the indexer (`init`, `increment`, `reprocess`, `erase`). Search and MCP navigation do not invoke it directly.
 
 The default embedding model is `sentence-transformers/all-MiniLM-L6-v2` (downloaded on first `init`). Override via the `EMBEDDING_MODEL` env var — see [`docs/CONFIGURATION.md` §1](./docs/CONFIGURATION.md#1-environment-variables).
 

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "java-codebase-rag"
-version = "0.2.0"
+version = "0.2.1"
 description = "MCP server for semantic + structural search over Java codebases"
 readme = "README.md"
 requires-python = ">=3.11"
@@ -23,6 +23,7 @@ classifiers = [
     "Topic :: Software Development :: Libraries",
 ]
 dependencies = [
+    "cocoindex[lancedb]>=1.0.0a43,<2",
     "kuzu>=0.11.3,<0.12",
     "lancedb>=0.25.3,<0.31",
     "mcp>=1.27.0,<2",

tests/test_agent_skills_static.py

@@ -16,8 +16,6 @@
 from pathlib import Path
 from typing import get_args
 
-import pytest
-
 from java_ontology import NodeKind
 from mcp_v2 import ComposedEdgeType, EdgeType
 
@@ -39,6 +37,7 @@
 
 SKILLS_DIR = Path(__file__).resolve().parent.parent / "skills"
 SKILL_NAME = "explore-codebase"
+EXPECTED_SKILL_DIRS = {"explore-codebase", "navigate-codebase"}
 SKILL_PATH = SKILLS_DIR / SKILL_NAME / "SKILL.md"
 
 
@@ -208,13 +207,13 @@ def test_readme_exists(self):
         assert (SKILLS_DIR / "README.md").is_file(), "skills/README.md missing"
 
     def test_no_other_skill_dirs(self):
-        """Only explore-codebase/ should exist as a skill directory."""
+        """Only documented consumer skill directories should exist."""
         skill_dirs = {
             p.name for p in SKILLS_DIR.iterdir()
             if p.is_dir() and (p / "SKILL.md").exists()
         }
-        assert skill_dirs == {SKILL_NAME}, (
-            f"Expected only skills/{SKILL_NAME}/, found: {skill_dirs}"
+        assert skill_dirs == EXPECTED_SKILL_DIRS, (
+            f"Expected only documented skills {EXPECTED_SKILL_DIRS}, found: {skill_dirs}"
         )
 
 

tests/test_packaging_metadata.py

@@ -0,0 +1,14 @@
+from __future__ import annotations
+
+import tomllib
+from pathlib import Path
+
+
+def test_published_package_installs_cocoindex_for_lifecycle_commands() -> None:
+    data = tomllib.loads((Path(__file__).resolve().parents[1] / "pyproject.toml").read_text())
+    deps = data["project"]["dependencies"]
+
+    cocoindex_deps = [dep for dep in deps if dep.startswith("cocoindex")]
+
+    assert cocoindex_deps
+    assert any("[lancedb]" in dep for dep in cocoindex_deps)